Chapter 6: Metabolism and Enzymes

 The sum total of an organism’s chemical reactions is called metabolism. The chemistry of life is organized into Metabolic Pathways

 Catabolic pathways release energy by breaking down complex molecules to simpler compounds Metabolic Pathways are made of: ATP

 Anabolic pathways consume energy to build complicated molecules from simpler compounds. Metabolic Pathways are made of: ATP

 Catabolic Pathways and Anabolic Pathways act in tandem Metabolic Pathways :

Fig. 6.1 The inset shows the first two steps in the catabolic pathway that breaks down glucose.

 Chemical reactions can be classified as either exergonic or endergonic based on energy.  An exergonic reaction proceeds with a net release of energy. Fig. 6.6a C 6 H 12 O 6 + 6O 2 -> 6CO 2 + 6H 2 O CATABOLIC PATHWAY Free energy of this reaction is negative (  G)

 An endergonic reaction is one that absorbs energy from its surroundings. –Endergonic reactions store energy ANABOLIC PATHWAY 6CO 2 + 6H 2 O -> C 6 H 12 O 6 + 6O 2 Free energy of this reaction is positive (  G)

 Exergonic Reactions and Endergonic Reactions are Coupled using ATP  ATP (adenosine triphosphate) is a type of nucleotide  ATP has the nitrogenous base adenine, the sugar ribose, and a chain of 3 phosphate groups ATP: Adenine Triphosphate

 Bonds between PO 4 groups can be broken to release energy  This is a hydrolysis reaction ATP: Adenosine Triphosphate

 PO 4 released is tagged to a reactant  Reactant is phosphorylated and now able to undergo the chemical reaction  ATP can be regenerated ATP: High NRG PO 4 Bond Transfer

 Energy Facts Energy is used by the cell for: Mechanical Work (movement), Transport (of macromolecules into and out of cells), and Chemical Work (drive endergonic reactions in anabolic pathways)  Plants transform light to chemical energy; they do not produce energy.

 Activation energy: Energy needed by reactants to make the products (NRG Barrier)  Activation Energy is used to make transition state complexes whose bonds are strained. Then, products form from these transition state complxes by breaking and making new bonds.

 Activation energy: Enzymes lower the Activation Energy needed for a reaction  Enzymes drive most chemical reactions in the body

 Activation energy: Enzymes lower the Activation Energy needed for a reaction  Enzymes drive most chemical reactions in the body Lactose > Glucose + Galactose Lactase (lactaid pills)

ENZYMES Enzyme discovery to benefit homeland security Enzymes are Proteins (names end in ase)

Enzymes:Are Substrate Specific  Enzyme names have 2 parts:  First part – which substrate it acts on/what product is formed  Second part – what it does Malate Dehydrogenase Citrate synthase

Enzymes:Are Substrate Specific 1. Oxidoreductases: Oxidation – reduction; (dehydrogenase, reductase, oxidase) 2. Transferases: Transfer functional groups; (transferase; phosphorylase) 3. Hydrolases: hydrolytic cleavage of C-O, C-N, C-C bonds (phosphatase; protease) 4. Lyases – cleave bonds (decarboxylase) 5. Isomerases - geometric or structural changes within a molecule (epimerase or isomerase) 6. Ligases - joining together of two molecules using ATP (synthetase; ligase) Skip details

Enzymes: Active Site Enzymes act on Substrates (reactants)  Active Site: is a pocket or groove on the surface of the enzyme into which the substrate fits (often active siteis a nonpolar environment)  Substrate binds to active site by hydrogen bonding/weak forces to form an enzyme- substrate complex

Enzymes: Active Sites  Active Site binding helps the reaction by: Substrates are placed in the correct orientation for the reaction. Puts stress on bonds that must be broken, making it easier to reach the transition state. R groups at the active site may create a conducive microenvironment for a specific reaction. Enzymes may even bind covalently to substrates in an intermediate step before returning to normal.

 Induced Fit Model For Enzyme Action:  Substrate binding to active site causes a change in enzyme shape around active site  The active site is molded into a tighter fit around the substrates  Substrates are held in close contact; E A is lowered; products are formed and released  Enzyme regains original shape; it is reused Enzymes: How do they work?

A single molecule of enzyme can catalyze 1000’s of reactions per second

 Enzymes can catalyze both forward and backward reactions  Direction of a reaction depends on accumulation/removal of product Enzymes: How do they work? Malate Dehydrogenase

 Substrate Concentration  Temperature  pH  Cofactors  Coenzymes  Competitive Inhibitors  Non-competitiveInhibitor  Allosteric Regulation and Co-operativity  Feedback Inhibition Enzymes: Factors affecting their function (nine of them! - know these)

Enzymes: Factors affecting their function The environment of the cell affects the structure of enzymes (proteins) at the secondary/tertiary/quarternary levels The effect is perceived as a change in reaction rate (rate of formation of product)

1) Substrate Concentration Enzymes: Factors affecting their function Low [S]: an increase in substrate speeds binding to available active sites ([E] >>>> [S]) High [S]: Enzyme is SATURATED (all active sites are occupied) (([S] >>>> [E]) At High [S]: To increase reaction rate, increase [E]

2) Temperature Enzymes: Factors affecting their function Low Temp: insufficient collisions between active site and substrates High Temp: Enzyme can denature and the folding can unravel, damaging functionality Optimal temp: Human enzymes – 37.5 o c

3) pH – determines state of acidic/basic functional ‘R’ groups on amino acids, and hydrogen bonding Enzymes: Factors affecting their function Low/High pH: changes the above interactions and alters folding of enzyme protein/active site Optimal pH: Human enzymes – pH 6-8

4) Cofactors –inorganic helpers. B ind permanently or reversibly to enzyme. What’s the biochemical reason? Examples: zinc, iron, and copper. Enzymes: Factors affecting their function Photosystem I multienzyme complexes

5) Coenzymes – organic helpers (same idea as cofactors). Bind reversibly to enzymes - can be re-used. Examples:vitamins. Enzymes: Factors affecting their function

 Inhibitors: 6) Competitive Inhibitors: Active Site Directed Inhibitors - bind to active site and inhibit binding of substrate Enzymes: Factors affecting their function

 Inhibitors: 7) NonCompetitive Inhibitors: Bind to a different site on enzyme called Allosteric Site - diminishes bindng of substrate to active site Enzymes: Factors affecting their function Minimata Bay – Japan (Mercury Poisoning) Nerve Gas Used on Kurds by Iraq

8) Allosteric Regulation: Enzyme has several subunits - hangs around in “active” or “inactive” state  Effect of binding of regulator (inhibitor/activator) to one subunit is translated to other subunits (cooperativity) Enzymes: Factors affecting their function

9) Feedback Inhibition - a metabolic pathway is turned off by its end product. End product becomes a inhibitor for a very early step enzyme. Very common! Enzymes: Factors affecting their function

Rate of a Reaction  Reaction Rate- the change in the concentration of a reactant or product with time. (M/s)  General equation for a reaction: –A → B –Reactant → Product  In order to monitor a reaction’s speed or rate, we can look at one of two things: –Decrease in [ reactant ] –Increase in [ product ] –Can be represented as: rate = - Δ [A] / Δ tor rate = Δ [B] / Δ t

Rate of a Reaction

Rate Calculations  How do we calculate the rate of a reaction? –We first need this information: Time (s) [reactant] Or [product] [ ] means concentration Decrease in [reactant]/time OR Increase in [product]/time Calculate the slope of your graph - X axis - time; Y axis - you choose (Y2-Y1)/(x2-x1)

Reaction rate calculation Initial Stage of Reaction: [Substrate] is: [Enzyme] is: Number of Active Sites available to catalyze this reaction is: Calculation of Initial Reaction rate: R i =( y 2 -y 1 )/(x 2 -x 1 ) => Rise/Run

Reaction rate calculation Final Stage of Reaction: [Substrate] is: [Enzyme] is: Number of Active Sites available to catalyze this reaction is: Calculation of Final Reaction rate: R f =( y 2 -y 1 )/(x 2 -x 1 ) = Maximum Velocity: Vmax